/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2020 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#ifndef _U2_MULTIPLE_ALIGNMENT_INFO_H_
#define _U2_MULTIPLE_ALIGNMENT_INFO_H_

#include <QString>
#include <QVariantMap>

#include <U2Core/global.h>

namespace U2 {

class U2CORE_EXPORT MultipleAlignmentInfo {
public:
    static const QString NAME;
    static const QString ACCESSION;
    static const QString DESCRIPTION;
    static const QString SS_CONSENSUS; /* Secondary structure consensus */
    static const QString REFERENCE_LINE; /* #=GC RF annotation in Stockholm markup */
    static const QString CUTOFFS; /* #=GF GA, NC, TC annotation in Stockholm markup */

    enum Cutoffs { /* Should be same as in esl_msa.h( uhmmer plugin ) */
                   CUTOFF_TC1,
                   CUTOFF_TC2,
                   CUTOFF_GA1,
                   CUTOFF_GA2,
                   CUTOFF_NC1,
                   CUTOFF_NC2
    };

    static bool isValid(const QVariantMap &map); /* Checks obligatory fields in info */

    static QString getName(const QVariantMap &map);
    static void setName(QVariantMap &map, const QString &name);
    static bool hasName(const QVariantMap &map);

    static QString getAccession(const QVariantMap &map);
    static void setAccession(QVariantMap &map, const QString &acc);
    static bool hasAccession(const QVariantMap &map);

    static QString getDescription(const QVariantMap &map);
    static void setDescription(QVariantMap &map, const QString &desc);
    static bool hasDescription(const QVariantMap &map);

    static QString getSSConsensus(const QVariantMap &map);
    static void setSSConsensus(QVariantMap &map, const QString &cs);
    static bool hasSSConsensus(const QVariantMap &map);

    static QString getReferenceLine(const QVariantMap &map);
    static void setReferenceLine(QVariantMap &map, const QString &rf);
    static bool hasReferenceLine(const QVariantMap &map);

    static float getCutoff(const QVariantMap &map, Cutoffs coff);
    static bool hasCutoff(const QVariantMap &map, Cutoffs coff);
    static void setCutoff(QVariantMap &map, Cutoffs coff, float val);
};

}    // namespace U2

#endif    // _U2_MULTIPLE_ALIGNMENT_INFO_H_
